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<h1 class="epydoc">Source Code for <a href="dadi.Demographics2D-module.html">Module dadi.Demographics2D</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring">Two population demographic models.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package dadi=dadi-module.html"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-0', 'dadi', 'link-0');">dadi</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module dadi.Numerics=dadi.Numerics-module.html"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-1', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Module dadi.PhiManip=dadi.PhiManip-module.html"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-2', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Module dadi.Integration=dadi.Integration-module.html"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-3', 'Integration', 'link-3');">Integration</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-4', 'dadi', 'link-0');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Module dadi.Spectrum_mod=dadi.Spectrum_mod-module.html"><a title="dadi.Spectrum_mod" class="py-name" href="#" onclick="return doclink('link-5', 'Spectrum_mod', 'link-5');">Spectrum_mod</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Variable dadi.Demographics1D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Variable dadi.Demographics2D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Class dadi.Spectrum_mod.Spectrum=dadi.Spectrum_mod.Spectrum-class.html"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-6', 'Spectrum', 'link-6');">Spectrum</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"> </tt>
<a name="snm"></a><div id="snm-def"><a name="L9"></a><tt class="py-lineno">  9</tt> <a class="py-toggle" href="#" id="snm-toggle" onclick="return toggle('snm');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#snm">snm</a><tt class="py-op">(</tt><tt class="py-param">notused</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="snm-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="snm-expanded"><a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,n2)</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring">    Standard neutral model, populations never diverge.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-7', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-8', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Function dadi.PhiManip.phi_1D()=dadi.PhiManip-module.html#phi_1D"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-9', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-10', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Function dadi.PhiManip.phi_1D_to_2D()=dadi.PhiManip-module.html#phi_1D_to_2D"><a title="dadi.PhiManip.phi_1D_to_2D" class="py-name" href="#" onclick="return doclink('link-11', 'phi_1D_to_2D', 'link-11');">phi_1D_to_2D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-12', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum.from_phi()=dadi.Spectrum_mod.Spectrum-class.html#from_phi"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-13', 'from_phi', 'link-13');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"> </tt>
<a name="bottlegrowth"></a><div id="bottlegrowth-def"><a name="L21"></a><tt class="py-lineno"> 21</tt> <a class="py-toggle" href="#" id="bottlegrowth-toggle" onclick="return toggle('bottlegrowth');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#bottlegrowth">bottlegrowth</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="bottlegrowth-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="bottlegrowth-expanded"><a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nuB,nuF,T)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,n2)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">    Instantanous size change followed by exponential growth with no population</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring">    split.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">    nuB: Ratio of population size after instantanous change to ancient</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">         population size</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    nuF: Ratio of contempoary to ancient population size</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past at which instantaneous change happened and growth began</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">       (in units of 2*Na generations) </tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">    n1,n2: Sample sizes of resulting Spectrum</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-name">nuB</tt><tt class="py-op">,</tt><tt class="py-name">nuF</tt><tt class="py-op">,</tt><tt class="py-name">T</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-14" class="py-name" targets="Function dadi.Demographics2D.bottlegrowth_split_mig()=dadi.Demographics2D-module.html#bottlegrowth_split_mig"><a title="dadi.Demographics2D.bottlegrowth_split_mig" class="py-name" href="#" onclick="return doclink('link-14', 'bottlegrowth_split_mig', 'link-14');">bottlegrowth_split_mig</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nuB</tt><tt class="py-op">,</tt><tt class="py-name">nuF</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"> </tt>
<a name="bottlegrowth_split"></a><div id="bottlegrowth_split-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="bottlegrowth_split-toggle" onclick="return toggle('bottlegrowth_split');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#bottlegrowth_split">bottlegrowth_split</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="bottlegrowth_split-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="bottlegrowth_split-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nuB,nuF,T,Ts)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,n2)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">    Instantanous size change followed by exponential growth then split.</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">    nuB: Ratio of population size after instantanous change to ancient</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">         population size</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring">    nuF: Ratio of contempoary to ancient population size</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past at which instantaneous change happened and growth began</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">       (in units of 2*Na generations) </tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">    Ts: Time in the past at which the two populations split.</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt class="py-docstring">    n1,n2: Sample sizes of resulting Spectrum</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt class="py-name">nuB</tt><tt class="py-op">,</tt><tt class="py-name">nuF</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">Ts</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-15" class="py-name"><a title="dadi.Demographics2D.bottlegrowth_split_mig" class="py-name" href="#" onclick="return doclink('link-15', 'bottlegrowth_split_mig', 'link-14');">bottlegrowth_split_mig</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">nuB</tt><tt class="py-op">,</tt><tt class="py-name">nuF</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">Ts</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
</div><a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"> </tt>
<a name="bottlegrowth_split_mig"></a><div id="bottlegrowth_split_mig-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="bottlegrowth_split_mig-toggle" onclick="return toggle('bottlegrowth_split_mig');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#bottlegrowth_split_mig">bottlegrowth_split_mig</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="bottlegrowth_split_mig-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="bottlegrowth_split_mig-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nuB,nuF,m,T,Ts)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,n2)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-docstring">    Instantanous size change followed by exponential growth then split with</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-docstring">    migration.</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">    nuB: Ratio of population size after instantanous change to ancient</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">         population size</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">    nuF: Ratio of contempoary to ancient population size</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">    m: Migration rate between the two populations (2*Na*m).</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past at which instantaneous change happened and growth began</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">       (in units of 2*Na generations) </tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">    Ts: Time in the past at which the two populations split.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">    n1,n2: Sample sizes of resulting Spectrum</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt class="py-name">nuB</tt><tt class="py-op">,</tt><tt class="py-name">nuF</tt><tt class="py-op">,</tt><tt class="py-name">m</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">Ts</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-16', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-17', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-18', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">    <tt class="py-name">nu_func</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-name">nuB</tt><tt class="py-op">*</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">nuF</tt><tt class="py-op">/</tt><tt class="py-name">nuB</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">t</tt><tt class="py-op">/</tt><tt class="py-name">T</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-19', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Function dadi.Integration.one_pop()=dadi.Integration-module.html#one_pop"><a title="dadi.Integration.one_pop" class="py-name" href="#" onclick="return doclink('link-20', 'one_pop', 'link-20');">one_pop</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">T</tt><tt class="py-op">-</tt><tt class="py-name">Ts</tt><tt class="py-op">,</tt> <tt class="py-name">nu_func</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-21', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="dadi.PhiManip.phi_1D_to_2D" class="py-name" href="#" onclick="return doclink('link-22', 'phi_1D_to_2D', 'link-11');">phi_1D_to_2D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-name">nu0</tt> <tt class="py-op">=</tt> <tt class="py-name">nu_func</tt><tt class="py-op">(</tt><tt class="py-name">T</tt><tt class="py-op">-</tt><tt class="py-name">Ts</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-name">nu_func</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-name">nu0</tt><tt class="py-op">*</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">nuF</tt><tt class="py-op">/</tt><tt class="py-name">nu0</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">t</tt><tt class="py-op">/</tt><tt class="py-name">Ts</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-23', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Function dadi.Integration.two_pops()=dadi.Integration-module.html#two_pops"><a title="dadi.Integration.two_pops" class="py-name" href="#" onclick="return doclink('link-24', 'two_pops', 'link-24');">two_pops</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">Ts</tt><tt class="py-op">,</tt> <tt class="py-name">nu_func</tt><tt class="py-op">,</tt> <tt class="py-name">nu_func</tt><tt class="py-op">,</tt> <tt class="py-name">m12</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt class="py-name">m21</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-25', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-26', 'from_phi', 'link-13');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"> </tt>
<a name="split_mig"></a><div id="split_mig-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="split_mig-toggle" onclick="return toggle('split_mig');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#split_mig">split_mig</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="split_mig-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="split_mig-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nu1,nu2,T,m)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,n2)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-docstring">    Split into two populations of specifed size, with migration.</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt class="py-docstring">    nu1: Size of population 1 after split.</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-docstring">    nu2: Size of population 2 after split.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past of split (in units of 2*Na generations) </tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"><tt class="py-docstring">    m: Migration rate between populations (2*Na*m)</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-docstring">    n1,n2: Sample sizes of resulting Spectrum</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">    <tt class="py-name">nu1</tt><tt class="py-op">,</tt><tt class="py-name">nu2</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-27', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-28', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-29', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-30', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="dadi.PhiManip.phi_1D_to_2D" class="py-name" href="#" onclick="return doclink('link-31', 'phi_1D_to_2D', 'link-11');">phi_1D_to_2D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-32', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="dadi.Integration.two_pops" class="py-name" href="#" onclick="return doclink('link-33', 'two_pops', 'link-24');">two_pops</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">T</tt><tt class="py-op">,</tt> <tt class="py-name">nu1</tt><tt class="py-op">,</tt> <tt class="py-name">nu2</tt><tt class="py-op">,</tt> <tt class="py-name">m12</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt class="py-name">m21</tt><tt class="py-op">=</tt><tt class="py-name">m</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line"> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-34', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-35', 'from_phi', 'link-13');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"> </tt>
<a name="split_mig_mscore"></a><div id="split_mig_mscore-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="split_mig_mscore-toggle" onclick="return toggle('split_mig_mscore');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#split_mig_mscore">split_mig_mscore</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="split_mig_mscore-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="split_mig_mscore-expanded"><a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"><tt class="py-docstring">    ms core command for split_mig.</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">    <tt class="py-name">nu1</tt><tt class="py-op">,</tt><tt class="py-name">nu2</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">    <tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-string">"-n 1 %(nu1)f -n 2 %(nu2)f "</tt>\ </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">            <tt class="py-string">"-ma x %(m12)f %(m21)f x "</tt>\ </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">            <tt class="py-string">"-ej %(T)f 2 1 -en %(T)f 1 1"</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">    <tt class="py-name">sub_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'nu1'</tt><tt class="py-op">:</tt><tt class="py-name">nu1</tt><tt class="py-op">,</tt> <tt class="py-string">'nu2'</tt><tt class="py-op">:</tt><tt class="py-name">nu2</tt><tt class="py-op">,</tt> <tt class="py-string">'m12'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt class="py-string">'m21'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt class="py-string">'T'</tt><tt class="py-op">:</tt> <tt class="py-name">T</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">}</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line"> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">command</tt> <tt class="py-op">%</tt> <tt class="py-name">sub_dict</tt> </tt>
</div><a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"> </tt>
<a name="IM"></a><div id="IM-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="IM-toggle" onclick="return toggle('IM');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#IM">IM</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IM-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IM-expanded"><a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,n2)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-docstring">    params = (s,nu1,nu2,T,m12,m21)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-docstring">    Isolation-with-migration model with exponential pop growth.</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-docstring">    s: Size of pop 1 after split. (Pop 2 has size 1-s.)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"><tt class="py-docstring">    nu1: Final size of pop 1.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-docstring">    nu2: Final size of pop 2.</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past of split (in units of 2*Na generations) </tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line"><tt class="py-docstring">    m12: Migration from pop 2 to pop 1 (2*Na*m12)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"><tt class="py-docstring">    m21: Migration from pop 1 to pop 2</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"><tt class="py-docstring">    n1,n2: Sample sizes of resulting Spectrum</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">    <tt class="py-name">s</tt><tt class="py-op">,</tt><tt class="py-name">nu1</tt><tt class="py-op">,</tt><tt class="py-name">nu2</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">m12</tt><tt class="py-op">,</tt><tt class="py-name">m21</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-36', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-37', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-38', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-39', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="dadi.PhiManip.phi_1D_to_2D" class="py-name" href="#" onclick="return doclink('link-40', 'phi_1D_to_2D', 'link-11');">phi_1D_to_2D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line"> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">    <tt class="py-name">nu1_func</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-name">s</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">nu1</tt><tt class="py-op">/</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">/</tt><tt class="py-name">T</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">    <tt class="py-name">nu2_func</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">nu2</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">/</tt><tt class="py-name">T</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-41', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="dadi.Integration.two_pops" class="py-name" href="#" onclick="return doclink('link-42', 'two_pops', 'link-24');">two_pops</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">T</tt><tt class="py-op">,</tt> <tt class="py-name">nu1_func</tt><tt class="py-op">,</tt> <tt class="py-name">nu2_func</tt><tt class="py-op">,</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">                               <tt class="py-name">m12</tt><tt class="py-op">=</tt><tt class="py-name">m12</tt><tt class="py-op">,</tt> <tt class="py-name">m21</tt><tt class="py-op">=</tt><tt class="py-name">m21</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line"> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-43', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-44', 'from_phi', 'link-13');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"> </tt>
<a name="IM_mscore"></a><div id="IM_mscore-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="IM_mscore-toggle" onclick="return toggle('IM_mscore');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#IM_mscore">IM_mscore</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IM_mscore-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IM_mscore-expanded"><a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-docstring">    ms core command for IM.</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">    <tt class="py-name">s</tt><tt class="py-op">,</tt><tt class="py-name">nu1</tt><tt class="py-op">,</tt><tt class="py-name">nu2</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">m12</tt><tt class="py-op">,</tt><tt class="py-name">m21</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">    <tt class="py-name">alpha1</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">nu1</tt><tt class="py-op">/</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">T</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">    <tt class="py-name">alpha2</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">nu2</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">T</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">    <tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-string">"-n 1 %(nu1)f -n 2 %(nu2)f "</tt>\ </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">            <tt class="py-string">"-eg 0 1 %(alpha1)f -eg 0 2 %(alpha2)f "</tt>\ </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">            <tt class="py-string">"-ma x %(m12)f %(m21)f x "</tt>\ </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">            <tt class="py-string">"-ej %(T)f 2 1 -en %(T)f 1 1"</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">    <tt class="py-name">sub_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'nu1'</tt><tt class="py-op">:</tt><tt class="py-name">nu1</tt><tt class="py-op">,</tt> <tt class="py-string">'nu2'</tt><tt class="py-op">:</tt><tt class="py-name">nu2</tt><tt class="py-op">,</tt> <tt class="py-string">'alpha1'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">alpha1</tt><tt class="py-op">,</tt> <tt class="py-string">'alpha2'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">alpha2</tt><tt class="py-op">,</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">                <tt class="py-string">'m12'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">m12</tt><tt class="py-op">,</tt> <tt class="py-string">'m21'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">m21</tt><tt class="py-op">,</tt> <tt class="py-string">'T'</tt><tt class="py-op">:</tt> <tt class="py-name">T</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">}</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">command</tt> <tt class="py-op">%</tt> <tt class="py-name">sub_dict</tt> </tt>
</div><a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"> </tt>
<a name="IM_pre"></a><div id="IM_pre-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="IM_pre-toggle" onclick="return toggle('IM_pre');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#IM_pre">IM_pre</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">,</tt> <tt class="py-param">ns</tt><tt class="py-op">,</tt> <tt class="py-param">pts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IM_pre-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IM_pre-expanded"><a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"><tt class="py-docstring">    params = (nuPre,TPre,s,nu1,nu2,T,m12,m21)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"><tt class="py-docstring">    ns = (n1,n2)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line"><tt class="py-docstring">    Isolation-with-migration model with exponential pop growth and a size change</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line"><tt class="py-docstring">    prior to split.</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line"><tt class="py-docstring">    nuPre: Size after first size change</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-docstring">    TPre: Time before split of first size change.</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-docstring">    s: Fraction of nuPre that goes to pop1. (Pop 2 has size nuPre*(1-s).)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"><tt class="py-docstring">    nu1: Final size of pop 1.</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"><tt class="py-docstring">    nu2: Final size of pop 2.</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"><tt class="py-docstring">    T: Time in the past of split (in units of 2*Na generations) </tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line"><tt class="py-docstring">    m12: Migration from pop 2 to pop 1 (2*Na*m12)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"><tt class="py-docstring">    m21: Migration from pop 1 to pop 2</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line"><tt class="py-docstring">    n1,n2: Sample sizes of resulting Spectrum</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line"><tt class="py-docstring">    pts: Number of grid points to use in integration.</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">    <tt class="py-name">nuPre</tt><tt class="py-op">,</tt><tt class="py-name">TPre</tt><tt class="py-op">,</tt><tt class="py-name">s</tt><tt class="py-op">,</tt><tt class="py-name">nu1</tt><tt class="py-op">,</tt><tt class="py-name">nu2</tt><tt class="py-op">,</tt><tt class="py-name">T</tt><tt class="py-op">,</tt><tt class="py-name">m12</tt><tt class="py-op">,</tt><tt class="py-name">m21</tt> <tt class="py-op">=</tt> <tt class="py-name">params</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">    <tt class="py-name">xx</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="dadi.Numerics" class="py-name" href="#" onclick="return doclink('link-45', 'Numerics', 'link-1');">Numerics</a></tt><tt class="py-op">.</tt><tt class="py-name">default_grid</tt><tt class="py-op">(</tt><tt class="py-name">pts</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-46', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="dadi.PhiManip.phi_1D" class="py-name" href="#" onclick="return doclink('link-47', 'phi_1D', 'link-9');">phi_1D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-48', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="dadi.Integration.one_pop" class="py-name" href="#" onclick="return doclink('link-49', 'one_pop', 'link-20');">one_pop</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">TPre</tt><tt class="py-op">,</tt> <tt class="py-name">nu</tt><tt class="py-op">=</tt><tt class="py-name">nuPre</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name"><a title="dadi.PhiManip" class="py-name" href="#" onclick="return doclink('link-50', 'PhiManip', 'link-2');">PhiManip</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="dadi.PhiManip.phi_1D_to_2D" class="py-name" href="#" onclick="return doclink('link-51', 'phi_1D_to_2D', 'link-11');">phi_1D_to_2D</a></tt><tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">phi</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">    <tt class="py-name">nu1_0</tt> <tt class="py-op">=</tt> <tt class="py-name">nuPre</tt><tt class="py-op">*</tt><tt class="py-name">s</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">    <tt class="py-name">nu2_0</tt> <tt class="py-op">=</tt> <tt class="py-name">nuPre</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">    <tt class="py-name">nu1_func</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-name">nu1_0</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">nu1</tt><tt class="py-op">/</tt><tt class="py-name">nu1_0</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">/</tt><tt class="py-name">T</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">    <tt class="py-name">nu2_func</tt> <tt class="py-op">=</tt> <tt class="py-keyword">lambda</tt> <tt class="py-name">t</tt><tt class="py-op">:</tt> <tt class="py-name">nu2_0</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">nu2</tt><tt class="py-op">/</tt><tt class="py-name">nu2_0</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">/</tt><tt class="py-name">T</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">    <tt class="py-name">phi</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="dadi.Integration" class="py-name" href="#" onclick="return doclink('link-52', 'Integration', 'link-3');">Integration</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="dadi.Integration.two_pops" class="py-name" href="#" onclick="return doclink('link-53', 'two_pops', 'link-24');">two_pops</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">xx</tt><tt class="py-op">,</tt> <tt class="py-name">T</tt><tt class="py-op">,</tt> <tt class="py-name">nu1_func</tt><tt class="py-op">,</tt> <tt class="py-name">nu2_func</tt><tt class="py-op">,</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">                               <tt class="py-name">m12</tt><tt class="py-op">=</tt><tt class="py-name">m12</tt><tt class="py-op">,</tt> <tt class="py-name">m21</tt><tt class="py-op">=</tt><tt class="py-name">m21</tt><tt class="py-op">)</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line"> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">    <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt id="link-54" class="py-name"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-54', 'Spectrum', 'link-6');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="dadi.Spectrum_mod.Spectrum.from_phi" class="py-name" href="#" onclick="return doclink('link-55', 'from_phi', 'link-13');">from_phi</a></tt><tt class="py-op">(</tt><tt class="py-name">phi</tt><tt class="py-op">,</tt> <tt class="py-name">ns</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">xx</tt><tt class="py-op">,</tt><tt class="py-name">xx</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">fs</tt> </tt>
</div><a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line"> </tt>
<a name="IM_pre_mscore"></a><div id="IM_pre_mscore-def"><a name="L219"></a><tt class="py-lineno">219</tt> <a class="py-toggle" href="#" id="IM_pre_mscore-toggle" onclick="return toggle('IM_pre_mscore');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="dadi.Demographics2D-module.html#IM_pre_mscore">IM_pre_mscore</a><tt class="py-op">(</tt><tt class="py-param">params</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IM_pre_mscore-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IM_pre_mscore-expanded"><a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line"><tt class="py-docstring">    ms core command for IM_pre.</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">    <tt class="py-name">nu1_0</tt> <tt class="py-op">=</tt> <tt class="py-name">nuPre</tt><tt class="py-op">*</tt><tt class="py-name">s</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-name">nu2_0</tt> <tt class="py-op">=</tt> <tt class="py-name">nuPre</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">    <tt class="py-name">alpha1</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">nu1</tt><tt class="py-op">/</tt><tt class="py-name">nu1_0</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">T</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">    <tt class="py-name">alpha2</tt> <tt class="py-op">=</tt> <tt class="py-name">numpy</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">(</tt><tt class="py-name">nu2</tt><tt class="py-op">/</tt><tt class="py-name">nu2_0</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">T</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">    <tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-string">"-n 1 %(nu1)f -n 2 %(nu2)f "</tt>\ </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">            <tt class="py-string">"-eg 0 1 %(alpha1)f -eg 0 2 %(alpha2)f "</tt>\ </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">            <tt class="py-string">"-ma x %(m12)f %(m21)f x "</tt>\ </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">            <tt class="py-string">"-ej %(T)f 2 1 -en %(T)f 1 %(nuP)f "</tt>\ </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">            <tt class="py-string">"-en %(TP)f 1 1"</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line"> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">    <tt class="py-name">sub_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'nu1'</tt><tt class="py-op">:</tt><tt class="py-name">nu1</tt><tt class="py-op">,</tt> <tt class="py-string">'nu2'</tt><tt class="py-op">:</tt><tt class="py-name">nu2</tt><tt class="py-op">,</tt> <tt class="py-string">'alpha1'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">alpha1</tt><tt class="py-op">,</tt> <tt class="py-string">'alpha2'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">alpha2</tt><tt class="py-op">,</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">                <tt class="py-string">'m12'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">m12</tt><tt class="py-op">,</tt> <tt class="py-string">'m21'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">m21</tt><tt class="py-op">,</tt> <tt class="py-string">'T'</tt><tt class="py-op">:</tt> <tt class="py-name">T</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">'nuP'</tt><tt class="py-op">:</tt><tt class="py-name">nuPre</tt><tt class="py-op">,</tt> <tt class="py-string">'TP'</tt><tt class="py-op">:</tt><tt class="py-name">TPre</tt><tt class="py-op">/</tt><tt class="py-number">2</tt><tt class="py-op">}</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line"> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">command</tt> <tt class="py-op">%</tt> <tt class="py-name">sub_dict</tt> </tt>
</div><a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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